Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing

R.A. Rienksma, M. Suarez Diez, H.J. Mollenkopf, G.M. Dolganov, A. Dorhoi, G.K. Schoolnik, V.A.P. Martins Dos Santos, S. Kaufmann, P.J. Schaap, M. Gengenbacher

Research output: Contribution to journalArticleAcademicpeer-review

43 Citations (Scopus)

Abstract

BackgroundThe human pathogen Mycobacterium tuberculosis has the capacity to escape eradication by professional phagocytes. During infection, M. tuberculosis resists the harsh environment of phagosomes and actively manipulates macrophages and dendritic cells to ensure prolonged intracellular survival. In contrast to other intracellular pathogens, it has remained difficult to capture the transcriptome of mycobacteria during infection due to an unfavorable host-to-pathogen ratio.ResultsWe infected the human macrophage-like cell line THP-1 with the attenuated M. tuberculosis surrogate M. bovis Bacillus Calmette¿Guérin (M. bovis BCG). Mycobacterial RNA was up to 1000-fold underrepresented in total RNA preparations of infected host cells. We employed microbial enrichment combined with specific ribosomal RNA depletion to simultaneously analyze the transcriptional responses of host and pathogen during infection by dual RNA sequencing. Our results confirm that mycobacterial pathways for cholesterol degradation and iron acquisition are upregulated during infection. In addition, genes involved in the methylcitrate cycle, aspartate metabolism and recycling of mycolic acids were induced. In response to M. bovis BCG infection, host cells upregulated de novo cholesterol biosynthesis presumably to compensate for the loss of this metabolite by bacterial catabolism.ConclusionsDual RNA sequencing allows simultaneous capture of the global transcriptome of host and pathogen, during infection. However, mycobacteria remained problematic due to their relatively low number per host cell resulting in an unfavorable bacterium-to-host RNA ratio. Here, we use a strategy that combines enrichment for bacterial transcripts and dual RNA sequencing to provide the most comprehensive transcriptome of intracellular mycobacteria to date. The knowledge acquired into the pathogen and host pathways regulated during infection may contribute to a solid basis for the deployment of novel intervention strategies to tackle infection
Original languageEnglish
Article number34
Number of pages31
JournalBMC Genomics
Volume16
DOIs
Publication statusPublished - 2015

Keywords

  • tuberculosis gene-expression
  • human macrophage infection
  • complete genome sequence
  • cholesterol catabolism
  • regulated genes
  • messenger-rna
  • acyl-coenzyme
  • in-vitro
  • host
  • pathogen

Fingerprint Dive into the research topics of 'Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing'. Together they form a unique fingerprint.

  • Datasets

    Microbe enriched dual RNA sequencing of Mycobacterium bovis BCG infecting macrophage-like THP-1 cells

    Rienksma, R. A. (Creator), Suarez Diez, M. (Creator), Mollenkopf, H. J. (Creator), Dolganov, G. M. (Creator), Dorhoi, A. (Creator), Schoolnik, G. K. (Creator), Martins dos Santos, V. (Creator), Kaufmann, S. (Creator), Schaap, P. (Creator) & Gengenbacher, M. (Creator), Wageningen University, 17 Jun 2014

    Dataset

    Cite this